Try   HackMD

Full workflow

Modular

TransformBOLD fitAnatomical fitRaw datasetTemplateFlowSlice-timingcorrectionResampledFieldmapResampledBOLDBOLD-to-T1wtransformHMCtransformsCoregistrationreferenceBOLD-fieldmaptransformMotioncorrectionreferencePreprocessedFieldmapT1w-to-templatetransformT1wBOLDSingle-bandreferenceFieldmapTemplate

Monolithic

PreprocessingRaw datasetTemplateFlowT1w-to-templatetransformBOLD-to-T1wtransformHMCtransformsCoregistrationreferenceBOLD-fieldmaptransformMotioncorrectionreferencePreprocessedfieldmapSlice-timingcorrectionResampledfieldmapResampledBOLDT1wBOLDSingle-bandreferenceFieldmapTemplate

Fit workflows

Anat and func

BOLD fitAnatomical fitRaw datasetTemplateFlowBOLD-to-T1wtransformHMCtransformsCoregistrationreferenceBOLD-fieldmaptransformMotioncorrectionreferencePreprocessedFieldmapT1w-to-templatetransformT1wBOLDSingle-bandreferenceFieldmapTemplate

Anat only

Anatomical fitRaw datasetTemplateFlowT1w-to-templatetransformT1wTemplate

Func only

BOLD fitRaw datasetBOLD-to-T1wtransformHMCtransformsCoregistrationreferenceBOLD-fieldmaptransformMotioncorrectionreferencePreprocessedFieldmapT1wBOLDSingle-bandreferenceFieldmap

Transform workflow

TransformFit derivativesRaw datasetSlice-timingcorrectionResampledFieldmapResampledBOLDT1w-to-templatetransformBOLD-to-T1wtransformHMCtransformsBOLD-fieldmaptransformPreprocessedFieldmapBOLD

Old

Fit derivatives
Raw dataset
T1w-to-template
                 transform
BOLD-to-T1w
         transform
Final BOLD
                                     Reference
Initial BOLD
                    Reference
Resampled
                     Fieldmap
HMC
                          transforms
BOLD mask
BOLD-fieldmap
                              transform
Preprocessed
                  Fieldmap
T1w
Fieldmap
BOLD
Single-band
         reference
Fit derivatives
Raw dataset
TemplateFlow
T1w-to-template
        transform
BOLD-to-T1w
         transform
HMC
       transforms
Final BOLD
                 Reference
BOLD-fieldmap
             transform
Initial BOLD
               Reference
Preprocessed
         Fieldmap
T1w
BOLD
Single-band
         reference
Fieldmap
Template

Fixup

Fit derivatives
Raw dataset
TemplateFlow
Manual fixes
T1w-to-template
        transform
BOLD-to-T1w
         transform
HMC
       transforms
Final BOLD
                 Reference
Initial BOLD
               Reference
Preprocessed
         Fieldmap
T1w
BOLD
Single-band
         reference
Fieldmap
Template
Brain Mask
BOLD-fieldmap
             transform

Optional template

Fit derivativesRaw datasetTemplateFlowT1w-to-templatetransformBOLD-to-T1wtransformHMCtransformsFinal BOLDReferenceBOLD-fieldmaptransformInitial BOLDReferencePreprocessedFieldmapT1wBOLDSingle-bandreferenceFieldmapTemplate

Bold preproc

Fit derivativesRaw datasetBOLD-to-T1wtransformHMCtransformsFinal BOLDReferenceBOLD-fieldmaptransformInitial BOLDReferencePreprocessedFieldmapT1wBOLDSingle-bandreferenceFieldmap
Last changed by 
 
Chris Markiewicz
0
75

Read more

Schema tests

Structure:

Jul 10, 2024
OHBM 2024 abstract

Title

Jun 4, 2024
Rethinking resampling - simultaneous head motion and susceptibility distortion correction

Here we consider the problem of applying susceptibility distortion correctionto EPI imaging data. We derive an efficient algorithm for simultaneouslycorrecting for head motion and susceptibility distortions.

Nov 12, 2023
General conventions for spatial derivatives

[

Sep 26, 2023
Read more from Chris Markiewicz
Published on HackMD